Bishop of Cork & Ross Dr John Buckley has said comments made by a priest at a funeral mass in the city were "offensive" and "entirely inappropriate".
Bishop Buckley was responding to complaints about a priest who asked mourners to pray that former Lord Mayor of Cork, John Murray would not be found guilty of sex assault charges.
In a statement, Bishop Buckley said the Diocese was unaware that these comments were going to be made, does not stand over them and sincerely regrets the obvious hurt they have caused.
Bishop Buckley said the Diocese fully respects the independence of the DPP and the Courts Service and regards it as entirely inappropriate that a funeral mass be used in such a manner.
The Diocese has been in touch with the priest's Order and expects it to address the issue.
The priest, who was a visiting Augustinian is understood to be a friend of the Murray family.
In a statement issued to RTÉ the head of the Augustinians in Ireland apologised for distress caused by the friar's comments.
Provincial Fr John Hennebry said the prayer was wholly inappropriate and has caused great distress.
He said what happened does not reflect in any way the sentiments of the Order with regard to child protection or due process for those who bring allegations of abuse or are accused of abuse.
Last Friday, Murray, who is 83, of Gregg Road in the City, was found guilty of the sexual assault of a teenager. He is to be sentenced on 2 December.